6IYI

X-ray sequence and high resolution crystal structure of Starry sturgeon methemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel X-ray sequences and crystal structures of Persian and Starry sturgeon methemoglobins: Highlighting the role of heme pocket waters in causing autoxidation.

Seyedarabi, A.Ariaeenejad, S.Moosavi-Movahedi, A.A.Rayati, S.Poursasan, N.Asiaie, N.Seraj, Z.Mehraban, F.Seyedarabi, S.E.

(2019) Biochim Biophys Acta Proteins Proteom 1867: 586-594

  • DOI: 10.1016/j.bbapap.2019.03.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although there is a high sequence similarity between mammalian and fish hemoglobin (Hb), the oxidation and heme loss rates can vary greatly between them such that fish Hbs oxidise much more rapidly than mammalian Hbs. There is to date no sequence or ...

    Although there is a high sequence similarity between mammalian and fish hemoglobin (Hb), the oxidation and heme loss rates can vary greatly between them such that fish Hbs oxidise much more rapidly than mammalian Hbs. There is to date no sequence or structural data for any sturgeon Hb to reveal the level of autoxidation in these fish. In this study, novel high resolution X-ray sequences and crystal structures of methemoglobin (Met-Hb) from two sturgeon fish including Persian sturgeon (Acipenser percisus) and Starry sturgeon (Acipenser stellatus) belonging to the Caspian sea has been determined. A comprehensive sequence and structure comparison between these sturgeon Met-Hbs and a number of non-sturgeon and normal and sickle cell anaemia human Hb in varying heme states has been carried out highlighting (i) the structural variability in the heme propionate groups; (ii) the existence of certain residues or their displacement and shift in the heme pocket allowing entry of water molecules into the heme pocket; (iii) the importance of the number of water molecules in the heme pocket; (iv) the hydrogen bonding between oxygens of A and D propionate groups and that of waters in the heme pocket; and (v) the role of heme binding waters causing oxidative stress and heme autoxidation.


    Organizational Affiliation

    Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran. Electronic address: a.seyedarabi@ut.ac.ir.,Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran.,Department of Chemistry, K. N. Toosi University of Technology, P.O. Box 16315-1618, Tehran 15418, Iran.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha chain
A
142Acipenser stellatusMutation(s): 0 
Find proteins for A0A1Z0YU11 (Acipenser stellatus)
Go to UniProtKB:  A0A1Z0YU11
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta chain
B
146Acipenser stellatusMutation(s): 0 
Find proteins for A0A1Z0YU12 (Acipenser stellatus)
Go to UniProtKB:  A0A1Z0YU12
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.138 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.980α = 90.00
b = 61.410β = 97.75
c = 102.366γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-12-16 
  • Released Date: 2019-04-10 
  • Deposition Author(s): Seyedarabi, A.
  • This entry supersedes: 5JNZ

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references